GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Sinorhizobium meliloti 1021

Align Phosphoglycerate mutase family protein, putative (characterized, see rationale)
to candidate SMc00006 SMc00006 hypothetical protein

Query= uniprot:N9V397
         (205 letters)



>FitnessBrowser__Smeli:SMc00006
          Length = 194

 Score = 63.5 bits (153), Expect = 2e-15
 Identities = 57/175 (32%), Positives = 88/175 (50%), Gaps = 25/175 (14%)

Query: 4   LILIRHGETEWNLLGKIQGCTDIELTPNGIQQA--NEVA-QQIKG----NFDIIYSSPLH 56
           + ++RHG+T+WN   ++QG  DI L   G QQA  N VA  +I G    +FD + SSPL 
Sbjct: 3   IYMVRHGQTDWNAESRLQGQKDIPLNETGRQQATGNGVALSRIIGSGAADFDFV-SSPLG 61

Query: 57  RALITAQKIAGDKEVHLI-----EGMKEIPFGTWEGHTFEELNGDINYK---KFLSGEDG 108
           R   T +++    ++  +     E +KE+ FG WEG+T  EL   +  +   + ++  D 
Sbjct: 62  RTRETMERLRRAMDLDPLAYRTDERLKEVSFGDWEGYTLPELKRLVPERIAERRVAKWDF 121

Query: 109 CP--FDSTGMSIASWSKKNAQLLLDLCKQNENKTIVCVSHGAWIKTSILGLLEME 161
            P   D+    I SW +  A L      ++  +  VCVSHG  I+     L EM+
Sbjct: 122 IPPGPDAESYEILSW-RVGAWL------RSVTRPTVCVSHGGVIRALFKLLGEMD 169


Lambda     K      H
   0.318    0.135    0.410 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 113
Number of extensions: 10
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 205
Length of database: 194
Length adjustment: 21
Effective length of query: 184
Effective length of database: 173
Effective search space:    31832
Effective search space used:    31832
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory